When running Apply with a single input file, Snekmer fails with the error message
InvalidIndexError in line 292 of /qfs/people/nitk592/snekmer-main/Snekmer/src/snekmer/snekmer/rules/apply.smk: Reindexing only valid with uniquely valued Index objects

It's currently possible to work around this issue by splitting the input into 2 or more fasta files.